The high adiabatic temperature rise and low heat dissipation rate of mass concrete will promote rapid hydration of the cementitious material and rapid consumption of water from the concrete pores, which may significantly accelerate the development of concrete autogenous shrinkage. In this study, the effect of the water-binder ratio on the autogenous shrinkage of C50 concrete mixed with MgO expansion agent (MEA) was explained with respect to mechanical properties, pore structure, degree of hydration, and micromorphology of the concrete based on a variable temperature curing chamber. The results show that the high temperature rise within the mass concrete accelerates the development of early (14 d) autogenous shrinkage of the concrete, and that the smaller the water-binder ratio, the greater the autogenous shrinkage of the concrete. With the addition of 8 wt% MEA, the autogenous shrinkage of concrete can be effectively compensated. The larger the water-binder ratio, the higher the degree of MgO hydration, and in terms of the compensation effect of autogenous shrinkage, the best performance is achieved at a water-binder ratio of 0.36. This study provides a data reference for the determination of the water-binder ratio in similar projects with MEA.